CrispRVariants (version 1.0.2)

barplotAlleleFreqs: Plots barplots of the spectrum of variants for a sample set

Description

For signature "matrix", this function optionally does a very naive classification of variants by size. Frameshift variant combinations are those whose sum is not divisible by three. Intron boundaries are *NOT* considered, use with caution! For signature "CrisprSet", the function uses the VariantAnnotation package to localize variant alleles with respect to annotated transcripts. Variants are annotated as "coding" when they are coding in any transcript.

(signature("CrisprSet")) Groups variants by size and type and produces a barplot showing the variant spectrum for each sample. Accepts all arguments accepted by barplotAlleleFreqs for signature("matrix"). Requires package "VariantAnnotation"

signature("matrix") Accepts a matrix of allele counts, with rownames being alleles and column names samples.

Usage

barplotAlleleFreqs(obj, ...)
"barplotAlleleFreqs"(obj, ..., txdb, min.freq = 0, include.chimeras = TRUE, group = NULL, palette = c("rainbow", "bluered"))
"barplotAlleleFreqs"(obj, category.labels = NULL, group = NULL, bar.colours = NULL, group.colours = NULL, legend.text.size = 10, axis.text.size = 10, legend.symbol.size = 1, snv.label = "SNV", novar.label = "no variant", chimera.label = "Other", include.table = TRUE, classify = TRUE)

Arguments

obj

The object to be plotted

...

additional arguments

txdb

A transcript database object

min.freq

Include variants with at frequency least min.freq in at least one sample. (Default: 0, i.e. no cutoff)

include.chimeras

Should chimeric reads be included in results? (Default: TRUE)

group

A grouping factor for the columns in obj. Columns in the same group will be displayed in the same text colour (Default: NULL)

palette

Colour palette. Options are "rainbow", a quantitative palette (default) or "bluered", a gradient palette.

category.labels

Labels for each category, corresponding to the rows of obj. Only applicable when categories are provided, i.e. "classify" is FALSE. (Default: NULL)

bar.colours

Colours for the categories in the barplot. Colours must be provided if there are more than 6 different categories.

group.colours

Colours for the text labels for the experimental groups A set of 15 different colours is provided.

legend.text.size

The size of the legend text, in points.

axis.text.size

The size of the axis text, in points

legend.symbol.size

The size of the symbols in the legend

snv.label

The row label for single nucleotide variants

novar.label

The row label for non-variant sequences

chimera.label

The row label for chimeric (non-linearly aligned) variant alleles

include.table

Should a table of allele (variant combination) counts and total sequences be plotted? (Default: TRUE)

classify

If TRUE, performs a naive classification by size (Default:TRUE)

Value

A ggplot2 barplot of the allele distribution and optionally a table of allele counts

Examples

data("gol_clutch1")
barplotAlleleFreqs(variantCounts(gol))

# Just show the barplot without the counts table:
barplotAlleleFreqs(variantCounts(gol), include.table = FALSE)